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CHECK report for ChAMPdata on malbec2

This page was generated on 2019-10-17 16:51:27 -0400 (Thu, 17 Oct 2019).

Package 54/371HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMPdata 2.16.0
Yuan Tian
Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_9
Last Commit: cf2dc5e
Last Changed Date: 2019-05-02 11:56:36 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.16.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChAMPdata_2.16.0.tar.gz
StartedAt: 2019-10-17 12:56:34 -0400 (Thu, 17 Oct 2019)
EndedAt: 2019-10-17 13:01:24 -0400 (Thu, 17 Oct 2019)
EllapsedTime: 289.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChAMPdata_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChAMPdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 743.0Mb
  sub-directories of 1Mb or more:
    data     619.3Mb
    extdata  123.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Error loading dataset 'bloodCtl':
   Error in nrow(x@elementMetadata) : 
    no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
  
  Error loading dataset 'myLoad':
   Error in nrow(x@elementMetadata) : 
    no slot of name "elementMetadata" for this object of class "MethylSet"
  
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChAMPdata-package 30.732  0.456  31.189
testDataSet       10.082  0.096  10.178
AnnoEPIC           5.414  0.035   5.449
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ChAMPdata’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChAMPdata)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K1.9230.0401.962
AnnoEPIC5.4140.0355.449
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0020.0000.002
ChAMPdata-package30.732 0.45631.189
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0000.0010.001
EPIC.manifest.hg194.7890.0624.851
EPIC.manifest.pop.hg193.2450.0373.281
EPICSimData2.1320.0842.216
MatchGeneName0.0180.0000.018
PathwayList0.3930.0000.393
bloodCtl0.0010.0000.001
hm450.manifest.hg191.7090.0121.721
hm450.manifest.pop.hg191.0720.0041.076
hprdAsigH2.4630.1562.619
illumina450Gr1.9590.0351.995
illuminaEPICGr2.5170.0052.521
multi.hit0.7990.0000.799
probe.features0.6770.0070.685
probe.features.epic1.6140.0011.614
probeInfoALL.epic.lv0.6720.0000.672
probeInfoALL.lv0.4780.0040.482
snp.hit0.8180.0000.818
testDataSet10.082 0.09610.178